Snapshot genomic surveillance reveals insights into antimicrobial resistance and lineage diversity of uropathogens in older adults in Queensland

Abstract Background Community-acquired urinary tract infections (UTIs) are a significant health concern in older adults. However, few studies have investigated the epidemiology of uropathogens across diverse settings where older adults reside. Methods In this study, we whole-genome sequenced urinary isolates of Escherichia coli, Klebsiella species, and Enterobacter cloacae complex collected from individuals aged 70 and over living in the community and residential aged care facilities (RACFs) in Queensland, Australia. We investigated the prevalence of antimicrobial resistance, pathogen population structure, and transmission dynamics across the settings. Results E. coli was most frequently identified (82.2%, 447/544), followed by K. pneumoniae (10.8%, 59/544) and E. hormaechei (2.6%, 14/544). Intra-species lineages were diverse, and a total of 177 sequence types were identified. The three predominant lineages were E. coli ST73 (10.7%, 54/504), ST95 (8.1%, 41/504), and ST131 (5.4%, 27/504). Transmission events were minimal, being identified in 13 patients (2.5%), mainly from the community. The resistance rate to antibiotics was low, with only a small proportion (9.7%) of multidrug-resistant (MDR) isolates. The predominant MDR lineage was E. coli ST131, which carried extended-spectrum beta-lactamase (ESBL) blaCTX-Mgenes. Conclusions Community-acquired urinary tract infections (UTIs) in older adults are predominantly caused by diverse E. coli lineages, with limited evidence of transmission within aged care facilities. The low rates of antimicrobial resistance in the community, along with the absence of strains adapted to a particular setting, suggest that current empiric therapy guidelines remain appropriate. Our prospective genomic surveillance offers valuable insights for monitoring UTIs in this population. It demonstrates the importance of an unbiased approach to accurately capture the prevalence and diversity of uropathogen lineages.